Chapter 10 Spirochaetota

10.1 MCI

GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) %>%
#  filter(time_point=="0_Wild") %>%
  group_by(diet) %>%
  summarise(MCI = mean(value), sd = sd(value)) %>%
  tt()
diet MCI sd
Post_grass 0.2396430 0.01304278
Pre_grass 0.2493529 0.01524032
Wild 0.2541861 0.02059163
MCI <- GIFTs_functions_community %>%
  rowMeans() %>%
  as_tibble(., rownames = "sample") %>%
  left_join(sample_metadata, by = join_by(sample == sample)) 
# %>% 
#   filter(diet!="Post_grass")

shapiro.test(MCI$value)

    Shapiro-Wilk normality test

data:  MCI$value
W = 0.98397, p-value = 0.8693
res.aov <- aov(value ~ diet, data=MCI)
summary(res.aov)
            Df   Sum Sq   Mean Sq F value Pr(>F)
diet         2 0.001317 0.0006583    2.39  0.107
Residuals   33 0.009090 0.0002755               

10.2 Community level plots

10.3 ANCOM-BC2

10.3.1 Captive vs Wild

10.3.1.1 Element level

10.4 Wilcoxon comparison

10.4.1 Community elements differences:

difference_table %>% 
  filter(group_color=="Wild") %>% 
  tt()
Elements Pre_grass Wild Function Element Difference group_color
D0702 2.176967e-01 4.215706e-01 Alcohol degradation_Ethanol Ethanol -0.2038739000 Wild
D0708 6.562387e-02 1.137517e-01 Alcohol degradation_Phytol Phytol -0.0481278300 Wild
D0705 2.174659e-01 2.932360e-01 Alcohol degradation_Propylene glycol Propylene glycol -0.0757701000 Wild
D0509 3.498560e-01 4.690221e-01 Amino acid degradation_Arginine Arginine -0.1191661000 Wild
D0505 2.884142e-01 3.728710e-01 Amino acid degradation_Valine Valine -0.0844568000 Wild
B0307 2.568247e-01 3.888024e-01 Amino acid derivative biosynthesis_Spermidine Spermidine -0.1319777000 Wild
D0903 1.047526e-03 2.363183e-03 Antibiotic degradation_Cephalosporin Cephalosporin -0.0013156570 Wild
D0904 3.904555e-05 1.422616e-03 Antibiotic degradation_Oxacillin Oxacillin -0.0013835705 Wild
B0902 9.761388e-06 3.556539e-04 Metallophore biosynthesis_Aerobactin Aerobactin -0.0003458925 Wild
D0608 3.360954e-04 1.404321e-02 Nitrogen compound degradation_Betaine Betaine -0.0137071121 Wild
D0306 2.292213e-01 3.300262e-01 Sugar degradation_D-Xylose D-Xylose -0.1008049000 Wild
D0806 2.616052e-05 9.531525e-04 Xenobiotic degradation_Anthranilate Anthranilate -0.0009269920 Wild
D0811 3.527381e-06 1.281851e-04 Xenobiotic degradation_Benzoyl-CoA Benzoyl-CoA -0.0001246577 Wild
D0808 1.952277e-06 7.113078e-05 Xenobiotic degradation_Cumate Cumate -0.0000691785 Wild
D0819 4.314553e-05 1.892106e-03 Xenobiotic degradation_Mercury Mercury -0.0018489605 Wild

10.4.1.1 Functional level

10.4.2 Before and after grass

10.4.2.1 Element level

10.4.2.2 Functional level

  taxon lfc_dietPre_grass p_dietPre_grass    Domain Function
1   S03        -0.1948368      0.01689626 Structure    Spore